EWAS
As
DMP_As_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'As_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_smk')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 23361
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 333
# Adjusted, p<0.05: 15990
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9130156
# Number of DMRs identified: 5
DMP_As_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_As_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'As_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 189
# Adjusted, p<0.05: 17770
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9489588
# Number of DMRs identified: 7
rm(DMP_As_age7_cordoverlap)
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
2
|
113992761
|
113993313
|
0
|
552
|
0
|
0.00e+00
|
8
|
|
3
|
46759437
|
46759698
|
0
|
261
|
0
|
8.00e-07
|
7
|
|
1
|
228395659
|
228396009
|
0
|
350
|
0
|
7.00e-07
|
5
|
|
17
|
1395863
|
1396123
|
0
|
260
|
0
|
2.00e-06
|
5
|
|
17
|
75315485
|
75315667
|
0
|
182
|
0
|
2.62e-05
|
6
|
No adjustment for fish consumption
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_smk/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_smk/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_smk/As_log2_manhattan_DMP_adj.png")

As, female
pDatAge7Metal_F = pDatAge7Metal[pDatAge7Metal$female_d == 1,]
pDatAge7Metal_F$race_child2 = as.factor(as.numeric(pDatAge7Metal_F$race_child2))
DMP_As_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'As_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F_smk')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 26064
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 16222
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9159963
# Number of DMRs identified: 4
DMP_As_F_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
pDatAge7Metal_F_cord = pDatAge7Metal_cord[pDatAge7Metal_cord$female_d == 1,]
pDatAge7Metal_F_cord$race_child2 = as.factor(as.numeric(pDatAge7Metal_F_cord$race_child2))
DMP_As_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'As_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 85
# Adjusted, p<0.05: 16601
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9435264
# Number of DMRs identified: 2
rm(DMP_As_F_age7_cordoverlap)
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
7
|
76027000
|
76027101
|
0.0e+00
|
101
|
0.0e+00
|
0.0000017
|
3
|
|
1
|
11561496
|
11561711
|
0.0e+00
|
215
|
0.0e+00
|
0.0000058
|
3
|
|
2
|
113992842
|
113993142
|
0.0e+00
|
300
|
0.0e+00
|
0.0000341
|
5
|
|
2
|
198651075
|
198651347
|
8.8e-06
|
272
|
8.8e-06
|
0.0127295
|
3
|
No adjustment for fish consumption
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F_smk/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F_smk/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_F_smk/As_log2_manhattan_DMP_adj.png")

As, male
pDatAge7Metal_M = pDatAge7Metal[pDatAge7Metal$female_d == 0,]
pDatAge7Metal_M$race_child2 = as.factor(as.numeric(pDatAge7Metal_M$race_child2))
DMP_As_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'As_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M_smk')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 11497
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 175
# Adjusted, p<0.05: 13972
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8382292
# Number of DMRs identified: 4
DMP_As_M_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
pDatAge7Metal_M_cord = pDatAge7Metal_cord[pDatAge7Metal_cord$female_d == 0,]
pDatAge7Metal_M_cord$race_child2 = as.factor(as.numeric(pDatAge7Metal_M_cord$race_child2))
DMP_As_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'As_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 104
# Adjusted, p<0.05: 17353
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9654988
# Number of DMRs identified: 7
rm(DMP_As_M_age7_cordoverlap)
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
47091977
|
47092178
|
0e+00
|
201
|
0e+00
|
0.0000001
|
4
|
|
8
|
22735275
|
22735478
|
0e+00
|
203
|
1e-07
|
0.0000619
|
4
|
|
2
|
164204751
|
164205032
|
1e-07
|
281
|
1e-07
|
0.0001212
|
4
|
|
16
|
88706240
|
88706389
|
8e-07
|
149
|
8e-07
|
0.0021312
|
2
|
No adjustment for fish consumption
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M_smk/As_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M_smk/As_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/As_M_smk/As_log2_manhattan_DMP_adj.png")

Ba
DMP_Ba_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Ba_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_smk')
Unadjusted, N = 333
Unadjusted, p<0.05: 11801
Unadjusted, FDR<0.05: 0
Unadjusted, pBonf<0.05: 0
Adjusted, N = 333
Adjusted, p<0.05: 12058
Adjusted, FDR<0.05: 0
Adjusted, pBonf<0.05: 0
Adjusted, lambda: 0.7933736
Number of DMRs identified: 3
DMP_Ba_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Ba_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Ba_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 189
# Adjusted, p<0.05: 14226
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8384028
# Number of DMRs identified: 4
rm(DMP_Ba_age7_cordoverlap)
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
6899084
|
6899577
|
0
|
493
|
0
|
0.0e+00
|
10
|
|
6
|
32145349
|
32145923
|
0
|
574
|
0
|
4.0e-07
|
20
|
|
16
|
1583809
|
1584118
|
0
|
309
|
0
|
4.6e-06
|
6
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_smk/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_smk/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_smk/Ba_log2_manhattan_DMP_adj.png")

Ba, female
DMP_Ba_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Ba_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F_smk')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 29651
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 23980
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.210756
# Number of DMRs identified: 6
DMP_Ba_F_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Ba_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Ba_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 85
# Adjusted, p<0.05: 26653
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.238713
# Number of DMRs identified: 4
rm(DMP_Ba_F_age7_cordoverlap)
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
6899084
|
6899577
|
0.0000000
|
493
|
0.0000000
|
0.0000000
|
10
|
|
17
|
37123637
|
37123949
|
0.0000000
|
312
|
0.0000000
|
0.0000011
|
9
|
|
22
|
30476088
|
30476345
|
0.0000000
|
257
|
0.0000001
|
0.0000450
|
8
|
|
2
|
183943387
|
183943551
|
0.0000000
|
164
|
0.0000001
|
0.0000863
|
5
|
|
8
|
144635308
|
144635610
|
0.0000005
|
302
|
0.0000005
|
0.0005899
|
8
|
|
7
|
94285269
|
94285288
|
0.0011747
|
19
|
0.0011747
|
1.0000000
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F_smk/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F_smk/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_F_smk/Ba_log2_manhattan_DMP_adj.png")

Ba, male
DMP_Ba_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Ba_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M_smk')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 25363
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 175
# Adjusted, p<0.05: 25117
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.190464
# Number of DMRs identified: 3
DMP_Ba_M_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Ba_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Ba_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 104
# Adjusted, p<0.05: 15406
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9304526
# Number of DMRs identified: 2
rm(DMP_Ba_M_age7_cordoverlap)
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
16
|
1583809
|
1584118
|
0e+00
|
309
|
0e+00
|
0.0000000
|
6
|
|
19
|
50194119
|
50194252
|
0e+00
|
133
|
0e+00
|
0.0000061
|
5
|
|
6
|
29595001
|
29595335
|
1e-07
|
334
|
1e-07
|
0.0001585
|
8
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M_smk/Ba_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M_smk/Ba_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Ba_M_smk/Ba_log2_manhattan_DMP_adj.png")

Cd
DMP_Cd_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cd_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_smk')
# # Unadjusted, N = 333
# Unadjusted, p<0.05: 9428
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 333
# Adjusted, p<0.05: 11898
# Adjusted, FDR<0.05: 1
# Adjusted, pBonf<0.05: 1
# Adjusted, lambda: 0.8219919
# Number of DMRs identified: 3
DMP_Cd_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Cd_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Cd_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 189
# Adjusted, p<0.05: 14918
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9046147
# Number of DMRs identified: 3
rm(DMP_Cd_age7_cordoverlap)
FDR-significant DMPs
|
|
cpg
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
112561
|
cg07044523
|
0.26 (0.17 ,0.34)
|
5.28
|
0
|
0.0021538
|
0.0022
|
chr1
|
153514376
|
S100A5
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
7
|
158045979
|
158046166
|
0
|
187
|
0
|
6.7e-06
|
3
|
|
5
|
23507449
|
23507656
|
0
|
207
|
0
|
9.6e-06
|
5
|
|
17
|
46685291
|
46685448
|
0
|
157
|
0
|
5.6e-05
|
5
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_smk/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_smk/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_smk/Cd_log2_manhattan_DMP_adj.png")

Cd, female
DMP_Cd_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cd_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F_smk')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 13276
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 13415
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8339903
# Number of DMRs identified: 6
DMP_Cd_F_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Cd_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Cd_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 85
# Adjusted, p<0.05: 17304
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9489797
# Number of DMRs identified: 7
rm(DMP_Cd_F_age7_cordoverlap)
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
6
|
32164926
|
32165321
|
0.0000000
|
395
|
0.0000000
|
0.0000000
|
7
|
|
17
|
46685291
|
46685448
|
0.0000000
|
157
|
0.0000000
|
0.0000008
|
5
|
|
6
|
1624385
|
1624442
|
0.0000001
|
57
|
0.0000001
|
0.0003821
|
2
|
|
5
|
23507449
|
23507656
|
0.0000001
|
207
|
0.0000001
|
0.0001196
|
5
|
|
11
|
73357094
|
73357276
|
0.0000020
|
182
|
0.0000025
|
0.0044181
|
6
|
|
5
|
132113754
|
132113860
|
0.0179428
|
106
|
0.0179428
|
1.0000000
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F_smk/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F_smk/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_F_smk/Cd_log2_manhattan_DMP_adj.png")

Cd, male
DMP_Cd_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cd_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M_smk')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 16666
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 175
# Adjusted, p<0.05: 21565
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.111181
# Number of DMRs identified: 3
# DMP_Cd_M_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Cd_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Cd_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 104
# Adjusted, p<0.05: 22052
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.140586
# Number of DMRs identified: 1
rm(DMP_Cd_M_age7_cordoverlap)
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
20
|
61446961
|
61447369
|
0.00e+00
|
408
|
0.00e+00
|
0.0000000
|
11
|
|
7
|
50518572
|
50518647
|
1.80e-06
|
75
|
2.80e-06
|
0.0096276
|
2
|
|
6
|
28446839
|
28447087
|
6.28e-05
|
248
|
6.28e-05
|
0.0951117
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M_smk/Cd_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M_smk/Cd_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cd_M_smk/Cd_log2_manhattan_DMP_adj.png")

Cr
DMP_Cr_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cr_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_smk')
# # Unadjusted, N = 333
# Unadjusted, p<0.05: 29723
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 333
# Adjusted, p<0.05: 23609
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.115003
# Number of DMRs identified: 5
DMP_Cr_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Cr_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Cr_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 189
# Adjusted, p<0.05: 19986
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.050624
# Number of DMRs identified: 4
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
5
|
145758709
|
145758881
|
0.00e+00
|
172
|
0.00e+00
|
0.0000182
|
4
|
|
16
|
66969473
|
66969500
|
0.00e+00
|
27
|
1.00e-07
|
0.0003708
|
2
|
|
6
|
33245769
|
33245990
|
7.00e-07
|
221
|
1.10e-06
|
0.0012157
|
7
|
|
19
|
50666378
|
50666538
|
2.37e-05
|
160
|
2.74e-05
|
0.0567867
|
3
|
|
6
|
33280198
|
33280228
|
2.74e-05
|
30
|
2.74e-05
|
0.3024815
|
3
|
No adjustment for fish consumption
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_smk/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_smk/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_smk/Cr_log2_manhattan_DMP_adj.png")

Cr, female
DMP_Cr_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cr_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F_smk')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 26701
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 24909
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.186951
# Number of identified DMR: 0
DMP_Cr_F_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Cr_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Cr_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 85
# Adjusted, p<0.05: 29235
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.299635
# Number of identified DMR: 0
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F_smk/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F_smk/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_F_smk/Cr_log2_manhattan_DMP_adj.png")

Cr, male
DMP_Cr_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cr_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M_smk')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 17887
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 175
# Adjusted, p<0.05: 12574
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8769853
# Number of DMRs identified: 1
DMP_Cr_M_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Cr_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Cr_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 104
# Adjusted, p<0.05: 14324
# Adjusted, FDR<0.05: 1
# Adjusted, pBonf<0.05: 1
# Adjusted, lambda: 0.874334
# Number of DMRs identified: 1
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
46685291
|
46685448
|
0
|
157
|
0
|
1.8e-06
|
5
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M_smk/Cr_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M_smk/Cr_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cr_M_smk/Cr_log2_manhattan_DMP_adj.png")

Cs
DMP_Cs_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cs_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_smk')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 16687
# Unadjusted, FDR<0.05: 4
# Unadjusted, pBonf<0.05: 2
# Adjusted, N = 333
# Adjusted, p<0.05: 13318
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8387198
# Number of DMRs identified: 5
DMP_Cs_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Cs_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Cs_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 189
# Adjusted, p<0.05: 13290
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8376426
# Number of DMRs identified: 5
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
13
|
47472049
|
47472429
|
0.0000000
|
380
|
0.0000001
|
0.0000226
|
12
|
|
6
|
33280051
|
33280228
|
0.0000000
|
177
|
0.0000001
|
0.0000553
|
6
|
|
10
|
94820922
|
94821085
|
0.0000001
|
163
|
0.0000001
|
0.0001480
|
6
|
|
6
|
32847761
|
32847845
|
0.0000449
|
84
|
0.0000561
|
0.1900047
|
7
|
|
20
|
57427641
|
57427762
|
0.0010524
|
121
|
0.0010524
|
0.9677029
|
6
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_smk/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_smk/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_smk/Cs_log2_manhattan_DMP_adj.png")

Cs, female
DMP_Cs_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cs_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F_smk')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 25871
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 16348
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9656277
# Number of DMRs identified: 3
DMP_Cs_F_age7[[3]]= NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Cs_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Cs_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 85
# Adjusted, p<0.05: 12170
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.7999635
# Number of DMRs identified: 2
rm(DMP_Cs_F_age7_cordoverlap);gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
1
|
200272111
|
200272215
|
0
|
104
|
0
|
2.10e-05
|
3
|
|
20
|
3145355
|
3145597
|
0
|
242
|
0
|
1.32e-05
|
3
|
|
6
|
29648378
|
29648628
|
0
|
250
|
0
|
3.89e-05
|
8
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F_smk/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F_smk/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_F_smk/Cs_log2_manhattan_DMP_adj.png")

Cs, male
DMP_Cs_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cs_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M_smk')
Unadjusted, N = 175
Unadjusted, p<0.05: 15896
Unadjusted, FDR<0.05: 0
Unadjusted, pBonf<0.05: 0
Adjusted, N = 175
Adjusted, p<0.05: 15716
Adjusted, FDR<0.05: 0
Adjusted, pBonf<0.05: 0
Adjusted, lambda: 0.9276189
Number of DMRs identified: 1
DMP_Cs_M_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Cs_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Cs_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 104
# Adjusted, p<0.05: 15813
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8980376
# Number of DMRs identified: 10
rm(DMP_Cs_M_age7_cordoverlap);gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
20
|
57427555
|
57427762
|
1.86e-05
|
207
|
1.86e-05
|
0.0347322
|
7
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M_smk/Cs_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M_smk/Cs_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cs_M_smk/Cs_log2_manhattan_DMP_adj.png")

Cu
DMP_Cu_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Cu_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_smk')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 10199
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 333
# Adjusted, p<0.05: 20001
# Adjusted, FDR<0.05: 29
# Adjusted, pBonf<0.05: 8
# Adjusted, lambda: 1.082819
# Number of DMRs identified: 18
DMP_Cu_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Cu_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Cu_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 189
# Adjusted, p<0.05: 18618
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.021546
# Number of identified DMR: 0
rm(DMP_Cu_age7_cordoverlap);gc()
FDR-significant DMPs
|
|
cpg
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
1551
|
cg00082497
|
-0.25 (-0.36 ,-0.15)
|
-5.32
|
2.8e-06
|
0.0375331
|
1.0000
|
chr1
|
32802133
|
MARCKSL1
|
|
2216
|
cg00116766
|
0.42 (0.28 ,0.56)
|
2.04
|
0.0e+00
|
0.0013289
|
0.0021
|
chr16
|
9857614
|
GRIN2A;GRIN2A;GRIN2A
|
|
15593
|
cg00908120
|
0.52 (0.33 ,0.7)
|
6.26
|
1.0e-07
|
0.0056610
|
0.0509
|
chr16
|
72872925
|
ZFHX3;ZFHX3
|
|
36122
|
cg02155957
|
0.38 (0.23 ,0.53)
|
3.25
|
7.0e-07
|
0.0150267
|
0.2705
|
chr1
|
46930731
|
|
|
66105
|
cg04015129
|
0.7 (0.44 ,0.96)
|
4.28
|
3.0e-07
|
0.0080222
|
0.1043
|
chr10
|
1058036
|
GTPBP4
|
|
76780
|
cg04692924
|
-0.42 (-0.59 ,-0.26)
|
-6.61
|
1.0e-06
|
0.0191351
|
0.4018
|
chr1
|
161720042
|
DUSP12
|
|
82479
|
cg05051957
|
-0.45 (-0.63 ,-0.28)
|
-5.60
|
4.0e-07
|
0.0105360
|
0.1686
|
chr8
|
141522459
|
CHRAC1;CHRAC1
|
|
96056
|
cg05955013
|
-0.4 (-0.55 ,-0.24)
|
-6.28
|
4.0e-07
|
0.0105360
|
0.1624
|
chr17
|
45056646
|
RPRML
|
|
107200
|
cg06723863
|
-0.26 (-0.36 ,-0.15)
|
-5.98
|
1.8e-06
|
0.0275171
|
0.7154
|
chr16
|
68270129
|
ESRP2;ESRP2
|
|
117957
|
cg07380021
|
-0.51 (-0.69 ,-0.32)
|
-5.42
|
1.0e-07
|
0.0056342
|
0.0451
|
chr1
|
206755252
|
RASSF5;RASSF5;RASSF5
|
|
124637
|
cg07831553
|
0.61 (0.36 ,0.86)
|
3.37
|
2.5e-06
|
0.0358634
|
1.0000
|
chr19
|
48796974
|
|
|
132730
|
cg08370347
|
0.51 (0.3 ,0.72)
|
3.91
|
1.7e-06
|
0.0266105
|
0.6653
|
chr5
|
171571793
|
STK10
|
|
157990
|
cg10145926
|
0.61 (0.39 ,0.84)
|
5.31
|
2.0e-07
|
0.0061658
|
0.0678
|
chr14
|
95875792
|
C14orf139
|
|
165306
|
cg10653573
|
0.82 (0.49 ,1.15)
|
5.43
|
1.4e-06
|
0.0251851
|
0.5541
|
chr8
|
141347297
|
TRAPPC9;TRAPPC9
|
|
168880
|
cg10923018
|
0.24 (0.16 ,0.32)
|
2.75
|
0.0e+00
|
0.0026797
|
0.0134
|
chr6
|
31743769
|
C6orf27
|
|
178008
|
cg11608893
|
0.61 (0.36 ,0.86)
|
6.05
|
1.6e-06
|
0.0266105
|
0.6420
|
chr6
|
32059542
|
TNXB
|
|
184513
|
cg12067421
|
-0.46 (-0.62 ,-0.31)
|
2.01
|
0.0e+00
|
0.0015700
|
0.0047
|
chr1
|
203246482
|
|
|
202444
|
cg13434714
|
-0.42 (-0.58 ,-0.26)
|
-5.77
|
8.0e-07
|
0.0172634
|
0.3280
|
chr12
|
6936787
|
LEPREL2
|
|
238372
|
cg15790767
|
1.05 (0.67 ,1.42)
|
3.84
|
1.0e-07
|
0.0042467
|
0.0297
|
chr6
|
13431216
|
GFOD1
|
|
257054
|
cg17143270
|
0.82 (0.51 ,1.14)
|
5.74
|
4.0e-07
|
0.0105360
|
0.1677
|
chr1
|
91532819
|
|
|
272331
|
cg18299835
|
-0.23 (-0.33 ,-0.14)
|
-4.13
|
2.1e-06
|
0.0304573
|
0.8223
|
chr19
|
13207445
|
NFIX
|
|
277756
|
cg18714712
|
-0.54 (-0.72 ,-0.36)
|
-5.97
|
0.0e+00
|
0.0013289
|
0.0027
|
chr19
|
49866917
|
DKKL1;TEAD2
|
|
288096
|
cg19532212
|
0.49 (0.31 ,0.67)
|
4.46
|
3.0e-07
|
0.0080222
|
0.1016
|
chr17
|
56769430
|
TEX14;RAD51C;TEX14;RAD51C
|
|
292461
|
cg19842134
|
-0.29 (-0.4 ,-0.17)
|
-3.53
|
9.0e-07
|
0.0178044
|
0.3561
|
chr12
|
54070591
|
ATP5G2;ATP5G2
|
|
299106
|
cg20365618
|
-0.24 (-0.34 ,-0.15)
|
0.42
|
1.5e-06
|
0.0262342
|
0.6034
|
chr10
|
121578384
|
INPP5F;INPP5F
|
|
338217
|
cg23477849
|
0.28 (0.19 ,0.38)
|
4.88
|
0.0e+00
|
0.0020266
|
0.0081
|
chr19
|
5698492
|
LONP1
|
|
370410
|
cg25954729
|
-0.22 (-0.3 ,-0.14)
|
-6.34
|
2.0e-07
|
0.0059844
|
0.0598
|
chr11
|
66610784
|
RCE1;C11orf80;RCE1
|
|
381104
|
cg26708724
|
0.66 (0.41 ,0.92)
|
6.73
|
5.0e-07
|
0.0120529
|
0.2049
|
chr4
|
187509785
|
FAT1
|
|
393045
|
cg27565067
|
0.48 (0.31 ,0.65)
|
6.20
|
0.0e+00
|
0.0029493
|
0.0177
|
chr17
|
149484
|
RPH3AL
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
22
|
45704901
|
45705265
|
0.0e+00
|
364
|
0.0e+00
|
0.0000000
|
7
|
|
20
|
35169538
|
35169886
|
0.0e+00
|
348
|
0.0e+00
|
0.0000000
|
6
|
|
16
|
66304366
|
66304585
|
0.0e+00
|
219
|
0.0e+00
|
0.0000001
|
3
|
|
10
|
121578136
|
121578639
|
0.0e+00
|
503
|
0.0e+00
|
0.0000001
|
4
|
|
12
|
54070516
|
54070610
|
0.0e+00
|
94
|
0.0e+00
|
0.0000006
|
5
|
|
16
|
8806530
|
8806756
|
0.0e+00
|
226
|
0.0e+00
|
0.0000004
|
7
|
|
17
|
149483
|
149488
|
0.0e+00
|
5
|
0.0e+00
|
0.0001527
|
2
|
|
6
|
1604012
|
1604212
|
0.0e+00
|
200
|
0.0e+00
|
0.0000163
|
5
|
|
20
|
3052114
|
3052483
|
0.0e+00
|
369
|
0.0e+00
|
0.0000189
|
9
|
|
17
|
1395863
|
1396123
|
0.0e+00
|
260
|
0.0e+00
|
0.0000409
|
5
|
|
19
|
55660590
|
55660625
|
0.0e+00
|
35
|
0.0e+00
|
0.0003053
|
4
|
|
15
|
100048370
|
100048500
|
0.0e+00
|
130
|
1.0e-07
|
0.0001014
|
3
|
|
2
|
130345204
|
130345405
|
0.0e+00
|
201
|
1.0e-07
|
0.0000974
|
3
|
|
17
|
47091977
|
47092178
|
1.0e-07
|
201
|
1.0e-07
|
0.0001424
|
4
|
|
19
|
50194119
|
50194252
|
1.0e-07
|
133
|
1.0e-07
|
0.0002345
|
5
|
|
13
|
100310161
|
100310405
|
1.0e-07
|
244
|
1.0e-07
|
0.0001709
|
4
|
|
11
|
19736149
|
19736333
|
1.0e-07
|
184
|
1.0e-07
|
0.0002923
|
5
|
|
1
|
207082827
|
207082900
|
1.1e-06
|
73
|
1.1e-06
|
0.0059448
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_smk/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_smk/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_smk/Cu_log2_manhattan_DMP_adj.png")

Cu, female
DMP_Cu_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Cu_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F_smk')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 19233
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 16152
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.952899
# Number of DMRs identified: 11
DMP_Cu_F_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Cu_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Cu_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 85
# Adjusted, p<0.05: 12980
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8014961
# Number of DMRs identified: 2
rm(DMP_Cu_F_age7_cordoverlap);gc
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
6
|
32063900
|
32064842
|
0.0000000
|
942
|
0.0000000
|
0.0000000
|
33
|
|
5
|
191295
|
191806
|
0.0000000
|
511
|
0.0000000
|
0.0000000
|
9
|
|
15
|
81426346
|
81426610
|
0.0000000
|
264
|
0.0000000
|
0.0000002
|
7
|
|
11
|
73357094
|
73357396
|
0.0000000
|
302
|
0.0000001
|
0.0000556
|
7
|
|
2
|
74875226
|
74875536
|
0.0000001
|
310
|
0.0000001
|
0.0000788
|
7
|
|
21
|
37442288
|
37442476
|
0.0000001
|
188
|
0.0000002
|
0.0002543
|
3
|
|
17
|
1395863
|
1396123
|
0.0000001
|
260
|
0.0000002
|
0.0001967
|
5
|
|
1
|
120174148
|
120174361
|
0.0000001
|
213
|
0.0000002
|
0.0002411
|
2
|
|
8
|
95962351
|
95962383
|
0.0000017
|
32
|
0.0000021
|
0.0210023
|
4
|
|
19
|
23941312
|
23941438
|
0.0001402
|
126
|
0.0001543
|
0.3553439
|
3
|
|
6
|
31734291
|
31734401
|
0.0007630
|
110
|
0.0007630
|
0.9352574
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F_smk/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F_smk/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_F_smk/Cu_log2_manhattan_DMP_adj.png")

Cu, male
DMP_Cu_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Cu_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M_smk')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 8255
# Unadjusted, FDR<0.05: 32
# Unadjusted, pBonf<0.05: 5
# Adjusted, N = 175
# Adjusted, p<0.05: 11939
# Adjusted, FDR<0.05: 49
# Adjusted, pBonf<0.05: 14
# Adjusted, lambda: 0.7284168
# Number of DMRs identified: 14
DMP_Cu_M_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Cu_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Cu_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 104
# Adjusted, p<0.05: 14082
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8571026
# Number of DMRs identified: 10
rm(DMP_Cu_M_age7_cordoverlap);gc
FDR-significant DMPs
|
|
cpg
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
15593
|
cg00908120
|
0.71 (0.47 ,0.96)
|
6.29
|
1.0e-07
|
0.0017621
|
0.0229
|
chr16
|
72872925
|
ZFHX3;ZFHX3
|
|
17338
|
cg01007589
|
0.91 (0.59 ,1.23)
|
4.79
|
1.0e-07
|
0.0030119
|
0.0422
|
chr19
|
49894178
|
CCDC155
|
|
18335
|
cg01063965
|
-0.27 (-0.37 ,-0.17)
|
-6.44
|
4.0e-07
|
0.0086883
|
0.1564
|
chr11
|
695461
|
TMEM80;TMEM80;DEAF1;DEAF1
|
|
24635
|
cg01447660
|
0.39 (0.23 ,0.54)
|
-0.92
|
1.9e-06
|
0.0224235
|
0.7624
|
chr2
|
69152678
|
|
|
25210
|
cg01485439
|
0.51 (0.31 ,0.7)
|
3.65
|
7.0e-07
|
0.0130637
|
0.2613
|
chr11
|
67225937
|
CABP4
|
|
36122
|
cg02155957
|
0.49 (0.29 ,0.68)
|
3.22
|
1.6e-06
|
0.0201772
|
0.6255
|
chr1
|
46930731
|
|
|
36678
|
cg02196294
|
-0.26 (-0.37 ,-0.15)
|
-5.41
|
4.2e-06
|
0.0349929
|
1.0000
|
chr6
|
39197260
|
KCNK5
|
|
41497
|
cg02490920
|
0.37 (0.24 ,0.51)
|
1.34
|
3.0e-07
|
0.0075004
|
0.1275
|
chr3
|
50304406
|
SEMA3B;SEMA3B
|
|
49479
|
cg02968175
|
0.31 (0.2 ,0.42)
|
5.76
|
2.0e-07
|
0.0053540
|
0.0857
|
chr16
|
4690020
|
MGRN1;MGRN1;MGRN1;MGRN1
|
|
61452
|
cg03717239
|
0.3 (0.18 ,0.42)
|
0.51
|
2.7e-06
|
0.0271495
|
1.0000
|
chr8
|
145574318
|
|
|
62678
|
cg03790745
|
0.28 (0.16 ,0.39)
|
5.56
|
3.5e-06
|
0.0321103
|
1.0000
|
chr11
|
63679432
|
RCOR2
|
|
66105
|
cg04015129
|
0.85 (0.56 ,1.13)
|
4.27
|
0.0e+00
|
0.0010425
|
0.0090
|
chr10
|
1058036
|
GTPBP4
|
|
72385
|
cg04406071
|
-0.3 (-0.41 ,-0.19)
|
-6.07
|
5.0e-07
|
0.0096730
|
0.1838
|
chr17
|
59489784
|
C17orf82
|
|
76780
|
cg04692924
|
-0.6 (-0.83 ,-0.37)
|
-6.58
|
1.0e-06
|
0.0158267
|
0.3957
|
chr1
|
161720042
|
DUSP12
|
|
82479
|
cg05051957
|
-0.62 (-0.86 ,-0.37)
|
-5.61
|
1.3e-06
|
0.0178448
|
0.5175
|
chr8
|
141522459
|
CHRAC1;CHRAC1
|
|
96056
|
cg05955013
|
-0.47 (-0.67 ,-0.28)
|
-6.30
|
2.7e-06
|
0.0271495
|
1.0000
|
chr17
|
45056646
|
RPRML
|
|
117957
|
cg07380021
|
-0.67 (-0.89 ,-0.45)
|
-5.43
|
0.0e+00
|
0.0010425
|
0.0047
|
chr1
|
206755252
|
RASSF5;RASSF5;RASSF5
|
|
132177
|
cg08329655
|
-0.44 (-0.6 ,-0.27)
|
-5.88
|
1.1e-06
|
0.0163083
|
0.4470
|
chr11
|
7534677
|
PPFIBP2
|
|
133940
|
cg08459368
|
0.58 (0.35 ,0.81)
|
2.70
|
1.7e-06
|
0.0203444
|
0.6510
|
chr11
|
61974948
|
SCGB2A1
|
|
138326
|
cg08760128
|
0.31 (0.19 ,0.42)
|
6.73
|
9.0e-07
|
0.0155789
|
0.3739
|
chr16
|
4723507
|
MGRN1;MGRN1;MGRN1;MGRN1
|
|
159790
|
cg10266648
|
1.06 (0.69 ,1.43)
|
5.98
|
1.0e-07
|
0.0017511
|
0.0210
|
chr2
|
106560529
|
|
|
168880
|
cg10923018
|
0.35 (0.24 ,0.46)
|
2.73
|
0.0e+00
|
0.0004255
|
0.0009
|
chr6
|
31743769
|
C6orf27
|
|
178008
|
cg11608893
|
0.95 (0.64 ,1.26)
|
6.08
|
0.0e+00
|
0.0010425
|
0.0042
|
chr6
|
32059542
|
TNXB
|
|
186947
|
cg12243007
|
0.46 (0.27 ,0.64)
|
-0.77
|
3.3e-06
|
0.0310915
|
1.0000
|
chr17
|
184018
|
RPH3AL
|
|
202444
|
cg13434714
|
-0.68 (-0.87 ,-0.48)
|
-5.78
|
0.0e+00
|
0.0000612
|
0.0001
|
chr12
|
6936787
|
LEPREL2
|
|
211983
|
cg13989834
|
0.55 (0.34 ,0.76)
|
3.14
|
9.0e-07
|
0.0146279
|
0.3364
|
chr9
|
134400392
|
UCK1;UCK1
|
|
232975
|
cg15389183
|
-0.22 (-0.31 ,-0.13)
|
-6.19
|
3.3e-06
|
0.0310915
|
1.0000
|
chr14
|
102829482
|
TECPR2;CINP
|
|
238372
|
cg15790767
|
1.16 (0.68 ,1.64)
|
3.86
|
4.2e-06
|
0.0349929
|
1.0000
|
chr6
|
13431216
|
GFOD1
|
|
242146
|
cg16068812
|
-1.01 (-1.42 ,-0.6)
|
-4.27
|
2.5e-06
|
0.0271495
|
0.9973
|
chr21
|
44528396
|
U2AF1;U2AF1;U2AF1
|
|
248112
|
cg16496814
|
0.28 (0.17 ,0.39)
|
5.22
|
1.1e-06
|
0.0163083
|
0.4461
|
chr11
|
9778721
|
|
|
250632
|
cg16656826
|
0.33 (0.2 ,0.45)
|
0.14
|
7.0e-07
|
0.0135857
|
0.2853
|
chr5
|
159343871
|
ADRA1B;ADRA1B
|
|
277216
|
cg18670846
|
0.73 (0.43 ,1.03)
|
-2.30
|
3.7e-06
|
0.0324333
|
1.0000
|
chr2
|
68917482
|
|
|
277756
|
cg18714712
|
-0.73 (-0.97 ,-0.48)
|
-5.95
|
0.0e+00
|
0.0010425
|
0.0094
|
chr19
|
49866917
|
DKKL1;TEAD2
|
|
281545
|
cg19005275
|
0.68 (0.45 ,0.92)
|
4.29
|
1.0e-07
|
0.0017511
|
0.0204
|
chr12
|
113588263
|
CCDC42B
|
|
288096
|
cg19532212
|
0.7 (0.45 ,0.95)
|
4.42
|
2.0e-07
|
0.0051395
|
0.0771
|
chr17
|
56769430
|
TEX14;RAD51C;TEX14;RAD51C
|
|
299106
|
cg20365618
|
-0.35 (-0.47 ,-0.23)
|
0.40
|
0.0e+00
|
0.0010425
|
0.0063
|
chr10
|
121578384
|
INPP5F;INPP5F
|
|
301945
|
cg20597842
|
0.99 (0.59 ,1.4)
|
5.88
|
3.1e-06
|
0.0308990
|
1.0000
|
chr12
|
7818585
|
APOBEC1
|
|
311691
|
cg21373263
|
0.79 (0.48 ,1.09)
|
3.29
|
8.0e-07
|
0.0146279
|
0.3254
|
chr10
|
126751982
|
CTBP2;CTBP2
|
|
317735
|
cg21864868
|
0.66 (0.4 ,0.91)
|
4.22
|
1.2e-06
|
0.0163083
|
0.4566
|
chr17
|
46673002
|
LOC404266;LOC404266;LOC404266;LOC404266;LOC404266
|
|
322216
|
cg22240394
|
1.07 (0.65 ,1.49)
|
6.82
|
1.4e-06
|
0.0183349
|
0.5500
|
chr3
|
186211630
|
|
|
322745
|
cg22286640
|
-0.78 (-1.1 ,-0.46)
|
-4.65
|
4.3e-06
|
0.0349929
|
1.0000
|
chr8
|
67026828
|
|
|
336099
|
cg23312431
|
0.34 (0.2 ,0.47)
|
-0.37
|
1.8e-06
|
0.0211836
|
0.6991
|
chr21
|
45773997
|
TRPM2
|
|
338217
|
cg23477849
|
0.39 (0.25 ,0.52)
|
4.90
|
1.0e-07
|
0.0017511
|
0.0202
|
chr19
|
5698492
|
LONP1
|
|
352329
|
cg24543538
|
0.84 (0.5 ,1.17)
|
3.22
|
2.0e-06
|
0.0228393
|
0.7994
|
chr2
|
241569846
|
GPR35
|
|
365034
|
cg25514328
|
-0.47 (-0.66 ,-0.27)
|
-4.77
|
3.6e-06
|
0.0321103
|
1.0000
|
chr17
|
78549324
|
RPTOR;RPTOR
|
|
370410
|
cg25954729
|
-0.31 (-0.41 ,-0.21)
|
-6.37
|
0.0e+00
|
0.0010425
|
0.0053
|
chr11
|
66610784
|
RCE1;C11orf80;RCE1
|
|
378724
|
cg26543311
|
1.1 (0.64 ,1.56)
|
7.17
|
4.4e-06
|
0.0357043
|
1.0000
|
chr12
|
48875427
|
C12orf54
|
|
381104
|
cg26708724
|
0.95 (0.63 ,1.27)
|
6.72
|
0.0e+00
|
0.0010425
|
0.0088
|
chr4
|
187509785
|
FAT1
|
|
392164
|
cg27503275
|
0.43 (0.26 ,0.61)
|
4.12
|
2.7e-06
|
0.0271495
|
1.0000
|
chr6
|
3880016
|
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
10
|
121578136
|
121578846
|
0.0000000
|
710
|
0.0000000
|
0.0000000
|
5
|
|
22
|
45704901
|
45705265
|
0.0000000
|
364
|
0.0000000
|
0.0000000
|
7
|
|
21
|
45773781
|
45773997
|
0.0000000
|
216
|
0.0000000
|
0.0000009
|
2
|
|
4
|
24796918
|
24797176
|
0.0000000
|
258
|
0.0000000
|
0.0000093
|
6
|
|
19
|
50194119
|
50194252
|
0.0000000
|
133
|
0.0000000
|
0.0000207
|
5
|
|
17
|
70723226
|
70723386
|
0.0000000
|
160
|
0.0000000
|
0.0000504
|
2
|
|
20
|
35169593
|
35169886
|
0.0000000
|
293
|
0.0000001
|
0.0000373
|
5
|
|
17
|
78549323
|
78549371
|
0.0000000
|
48
|
0.0000001
|
0.0003164
|
3
|
|
3
|
16216093
|
16216215
|
0.0000001
|
122
|
0.0000001
|
0.0002044
|
4
|
|
14
|
78447480
|
78447640
|
0.0000001
|
160
|
0.0000001
|
0.0001737
|
3
|
|
17
|
149483
|
149488
|
0.0000001
|
5
|
0.0000002
|
0.0111041
|
2
|
|
10
|
135051232
|
135051351
|
0.0000006
|
119
|
0.0000007
|
0.0020801
|
7
|
|
12
|
54070516
|
54070591
|
0.0000107
|
75
|
0.0000115
|
0.0546485
|
4
|
|
16
|
8806689
|
8806756
|
0.0003889
|
67
|
0.0003889
|
0.8987147
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M_smk/Cu_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M_smk/Cu_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Cu_M_smk/Cu_log2_manhattan_DMP_adj.png")

Hg
DMP_Hg_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Hg_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_smk')
# Unadjusted, N = 326
# Unadjusted, p<0.05: 37293
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 326
# Adjusted, p<0.05: 26572
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.213221
# Number of DMRs identified: 4
DMP_Hg_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Hg_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Hg_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 186
# Adjusted, p<0.05: 25003
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.148742
# Number of DMRs identified: 3
rm(DMP_Hg_age7_cordoverlap);gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
46681110
|
46681401
|
0.00e+00
|
291
|
0.00e+00
|
0.0000009
|
6
|
|
6
|
31846768
|
31847009
|
0.00e+00
|
241
|
0.00e+00
|
0.0000034
|
9
|
|
10
|
131843516
|
131843798
|
0.00e+00
|
282
|
0.00e+00
|
0.0000112
|
4
|
|
3
|
42977888
|
42978026
|
2.93e-05
|
138
|
2.93e-05
|
0.0802830
|
4
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_smk/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_smk/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_smk/Hg_log2_manhattan_DMP_adj.png")

Hg, female
DMP_Hg_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Hg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F_smk')
# Unadjusted, N = 154
# Unadjusted, p<0.05: 35686
# Unadjusted, FDR<0.05: 156
# Unadjusted, pBonf<0.05: 1
# Adjusted, N = 154
# Adjusted, p<0.05: 15090
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8796583
# Number of DMRs identified: 3
DMP_Hg_F_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Hg_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Hg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 83
# Adjusted, p<0.05: 11644
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.7673862
# Number of DMRs identified: 2
rm(DMP_Hg_F_age7_cordoverlap);gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
12
|
47219625
|
47220092
|
0e+00
|
467
|
0e+00
|
0.0000001
|
12
|
|
4
|
165877874
|
165878136
|
0e+00
|
262
|
0e+00
|
0.0000008
|
6
|
|
7
|
27143234
|
27143478
|
1e-07
|
244
|
1e-07
|
0.0001227
|
7
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F_smk/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F_smk/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_F_smk/Hg_log2_manhattan_DMP_adj.png")

Hg, male
DMP_Hg_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Hg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M_smk')
# Unadjusted, N = 172
# Unadjusted, p<0.05: 22412
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 172
# Adjusted, p<0.05: 24091
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.207859
# Number of DMRs identified: 9
DMP_Hg_M_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Hg_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Hg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 103
# Adjusted, p<0.05: 24791
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.169208
# Number of DMRs identified: 5
rm(DMP_Hg_M_age7_cordoverlap);gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
6
|
31846768
|
31847009
|
0.0000000
|
241
|
0.0000000
|
0.0000000
|
9
|
|
11
|
18477152
|
18477534
|
0.0000000
|
382
|
0.0000000
|
0.0000001
|
7
|
|
11
|
18433499
|
18433887
|
0.0000000
|
388
|
0.0000000
|
0.0000001
|
5
|
|
5
|
502290
|
502571
|
0.0000000
|
281
|
0.0000000
|
0.0000004
|
3
|
|
6
|
33282735
|
33283162
|
0.0000000
|
427
|
0.0000000
|
0.0000011
|
20
|
|
14
|
104690039
|
104690244
|
0.0000000
|
205
|
0.0000000
|
0.0000129
|
5
|
|
1
|
147737015
|
147737207
|
0.0000001
|
192
|
0.0000002
|
0.0002762
|
4
|
|
1
|
2345151
|
2345410
|
0.0000002
|
259
|
0.0000002
|
0.0002468
|
8
|
|
1
|
117317981
|
117318133
|
0.0011583
|
152
|
0.0011583
|
0.9505995
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M_smk/Hg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M_smk/Hg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Hg_M_smk/Hg_log2_manhattan_DMP_adj.png")

Mg
DMP_Mg_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Mg_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_smk')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 18232
# Unadjusted, FDR<0.05: 1
# Unadjusted, pBonf<0.05: 1
# Adjusted, N = 333
# Adjusted, p<0.05: 15821
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8746056
# Number of DMRs identified: 5
DMP_Mg_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Mg_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Mg_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 189
# Adjusted, p<0.05: 16543
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9351369
# Number of DMRs identified: 2
rm(DMP_Mg_age7_cordoverlap);gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
20
|
3051953
|
3052345
|
0.0000000
|
392
|
0.0000000
|
0.0000000
|
9
|
|
6
|
31543539
|
31543686
|
0.0000000
|
147
|
0.0000000
|
0.0000353
|
8
|
|
2
|
240196768
|
240196996
|
0.0000001
|
228
|
0.0000001
|
0.0000921
|
3
|
|
11
|
368564
|
368712
|
0.0000014
|
148
|
0.0000017
|
0.0035951
|
7
|
|
6
|
10884093
|
10884140
|
0.0007239
|
47
|
0.0007239
|
0.9977073
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_smk/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_smk/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_smk/Mg_log2_manhattan_DMP_adj.png")

Mg, female
DMP_Mg_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Mg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F_smk')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 33977
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 20594
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.079708
# Number of DMRs identified: 2
DMP_Mg_F_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Mg_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Mg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 85
# Adjusted, p<0.05: 17171
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9523752
# Number of DMRs identified: 3
rm(DMP_Mg_F_age7_cordoverlap);gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
2
|
240196876
|
240196996
|
0.0000008
|
120
|
0.0000017
|
0.0027396
|
2
|
|
6
|
10884093
|
10884140
|
0.0001867
|
47
|
0.0001867
|
0.7913380
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F_smk/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F_smk/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_F_smk/Mg_log2_manhattan_DMP_adj.png")

Mg, male
DMP_Mg_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Mg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M_smk')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 9395
# Unadjusted, FDR<0.05: 7
# Unadjusted, pBonf<0.05: 5
# Adjusted, N = 175
# Adjusted, p<0.05: 13551
# Adjusted, FDR<0.05: 3
# Adjusted, pBonf<0.05: 3
# Adjusted, lambda: 0.8048792
# Number of identified DMR: 2
DMP_Mg_M_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Mg_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Mg_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 104
# Adjusted, p<0.05: 14864
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8507625
# Number of DMRs identified: 5
rm(DMP_Mg_M_age7_cordoverlap);gc()
FDR-significant DMPs
|
|
cpg
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
202444
|
cg13434714
|
-0.6 (-0.79 ,-0.41)
|
-5.78
|
0
|
0.0016633
|
0.0017
|
chr12
|
6936787
|
LEPREL2
|
|
277216
|
cg18670846
|
0.84 (0.56 ,1.12)
|
-2.30
|
0
|
0.0030248
|
0.0060
|
chr2
|
68917482
|
|
|
381104
|
cg26708724
|
0.89 (0.58 ,1.19)
|
6.72
|
0
|
0.0059299
|
0.0178
|
chr4
|
187509785
|
FAT1
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
5
|
23507449
|
23507656
|
0
|
207
|
0
|
6.62e-05
|
5
|
|
17
|
37123668
|
37123949
|
0
|
281
|
0
|
5.24e-05
|
8
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M_smk/Mg_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M_smk/Mg_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mg_M_smk/Mg_log2_manhattan_DMP_adj.png")

Mn
DMP_Mn_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Mn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_smk')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 27983
# Unadjusted, FDR<0.05: 6
# Unadjusted, pBonf<0.05: 1
# Adjusted, N = 333
# Adjusted, p<0.05: 37788
# Adjusted, FDR<0.05: 13
# Adjusted, pBonf<0.05: 3
# Adjusted, lambda: 1.339163
# Number of DMRs identified: 10
DMP_Mn_age7[[3]] = NULL
# limma on Beta-values
DMP_Mn_age7_beta = run_EWAS(DNAm = ComBat.Betas.Metals, pheno = pDatAge7Metal, var = 'Mn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_smk_beta')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 34004
# Unadjusted, FDR<0.05: 2096
# Unadjusted, pBonf<0.05: 39
# Adjusted, N = 333
# Adjusted, p<0.05: 42632
# Adjusted, FDR<0.05: 5339
# Adjusted, pBonf<0.05: 75
# Adjusted, lambda: 1.240793
# Number of DMRs identified: 121
DMP_Mn_age7_beta[[3]][DMP_Mn_age7_beta[[3]]$cpg == 'cg02042823',c(2:4)]*100
# logFC CI.L CI.R
# cg02042823 0.7500762 0.1418274 1.358325
rm(DMP_Mn_age7_beta);gc()
# Sensitivity analysis only including overlap with cord blood infants
DMP_Mn_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Mn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 189
# Adjusted, p<0.05: 39204
# Adjusted, FDR<0.05: 65
# Adjusted, pBonf<0.05: 8
# Adjusted, lambda: 1.310818
# Number of DMRs identified: 9
rm(DMP_Mn_age7_cordoverlap);gc()
FDR-significant DMPs
|
|
cpg
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
13985
|
cg00808511
|
0.18 (0.11 ,0.25)
|
2.86
|
1.5e-06
|
0.0441289
|
0.5737
|
chr16
|
52495237
|
TOX3;TOX3
|
|
61437
|
cg03716590
|
0.18 (0.11 ,0.25)
|
5.09
|
9.0e-07
|
0.0357372
|
0.3580
|
chr7
|
95435309
|
DYNC1I1;DYNC1I1;DYNC1I1
|
|
90890
|
cg05613017
|
0.2 (0.12 ,0.28)
|
5.33
|
5.0e-07
|
0.0310721
|
0.2156
|
chr12
|
65589446
|
LEMD3;LEMD3
|
|
153815
|
cg09856068
|
-0.11 (-0.16 ,-0.07)
|
-4.37
|
8.0e-07
|
0.0357372
|
0.3012
|
chr5
|
170878246
|
FGF18
|
|
170758
|
cg11063328
|
-0.16 (-0.22 ,-0.1)
|
-6.02
|
6.0e-07
|
0.0310721
|
0.2175
|
chr11
|
18343203
|
GTF2H1;HPS5;HPS5;HPS5;GTF2H1
|
|
209344
|
cg13834844
|
-0.1 (-0.14 ,-0.06)
|
-5.14
|
1.0e-07
|
0.0138786
|
0.0555
|
chr10
|
102415320
|
|
|
216559
|
cg14252211
|
0.2 (0.13 ,0.26)
|
5.85
|
0.0e+00
|
0.0023306
|
0.0047
|
chr1
|
25919394
|
|
|
286458
|
cg19407717
|
0.31 (0.22 ,0.4)
|
4.03
|
0.0e+00
|
0.0000169
|
0.0000
|
chr2
|
1544120
|
TPO;TPO;TPO;TPO
|
|
286677
|
cg19425870
|
-0.15 (-0.21 ,-0.09)
|
-6.46
|
1.0e-06
|
0.0357372
|
0.3931
|
chr11
|
3876808
|
STIM1
|
|
326256
|
cg22586726
|
0.27 (0.16 ,0.38)
|
-0.97
|
1.3e-06
|
0.0424978
|
0.5100
|
chr10
|
134150542
|
LRRC27;LRRC27;LRRC27;LRRC27;LRRC27
|
|
347861
|
cg24196240
|
0.33 (0.21 ,0.45)
|
5.25
|
1.0e-07
|
0.0114167
|
0.0343
|
chr21
|
36096009
|
NCRNA00160
|
|
359777
|
cg25101184
|
0.25 (0.15 ,0.34)
|
3.38
|
8.0e-07
|
0.0357372
|
0.3286
|
chr14
|
56231604
|
RPL13AP3
|
|
386595
|
cg27095984
|
-0.19 (-0.26 ,-0.12)
|
5.27
|
3.0e-07
|
0.0216665
|
0.1083
|
chr13
|
21652115
|
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
10
|
134150488
|
134150760
|
0.0000000
|
272
|
0.0000000
|
0.0000000
|
7
|
|
19
|
21657528
|
21657756
|
0.0000000
|
228
|
0.0000000
|
0.0000002
|
4
|
|
16
|
30572738
|
30573013
|
0.0000000
|
275
|
0.0000000
|
0.0000004
|
5
|
|
10
|
45406680
|
45406847
|
0.0000000
|
167
|
0.0000000
|
0.0000545
|
3
|
|
16
|
73100425
|
73100510
|
0.0000000
|
85
|
0.0000000
|
0.0001310
|
2
|
|
11
|
76839190
|
76839476
|
0.0000000
|
286
|
0.0000000
|
0.0000395
|
4
|
|
20
|
61659979
|
61660250
|
0.0000001
|
271
|
0.0000001
|
0.0001260
|
2
|
|
15
|
91473290
|
91473386
|
0.0000226
|
96
|
0.0000282
|
0.0885929
|
3
|
|
10
|
35484767
|
35484824
|
0.0003062
|
57
|
0.0003402
|
0.8798961
|
3
|
|
10
|
530950
|
531098
|
0.0019955
|
148
|
0.0019955
|
0.9951256
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_smk/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_smk/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_smk/Mn_log2_manhattan_DMP_adj.png")

Mn, female
DMP_Mn_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F_smk')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 28256
# Unadjusted, FDR<0.05: 3
# Unadjusted, pBonf<0.05: 3
# Adjusted, N = 158
# Adjusted, p<0.05: 39831
# Adjusted, FDR<0.05: 6
# Adjusted, pBonf<0.05: 2
# Adjusted, lambda: 1.354546
# Number of DMRs identified: 1
DMP_Mn_F_age7[[3]] = NULL
# limma on Beta-values
DMP_Mn_F_age7_beta = run_EWAS(DNAm = ComBat.Betas.Metals, pheno = pDatAge7Metal_F, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F_smk_beta')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 34431
# Unadjusted, FDR<0.05: 3379
# Unadjusted, pBonf<0.05: 42
# Adjusted, N = 158
# Adjusted, p<0.05: 43301
# Adjusted, FDR<0.05: 7595
# Adjusted, pBonf<0.05: 69
# Adjusted, lambda: 1.248445
# Number of DMRs identified: 171
DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg00954161',c(2:4)]*100
# logFC CI.L CI.R
# cg00954161 1.333573 0.6920163 1.975131
DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg11161853',c(2:4)]*100
# logFC CI.L CI.R
# cg11161853 0.00902998 -0.05582495 0.07388491
DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg23903787',c(2:4)]*100
# logFC CI.L CI.R
# cg23903787 2.035622 0.7851984 3.286046
DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg19908812',c(2:4)]*100
# logFC CI.L CI.R
# cg19908812 -0.03226102 -0.3388754 0.2743534
DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg26462130',c(2:4)]*100
# logFC CI.L CI.R
# cg26462130 0.9842899 0.6837261 1.284854
DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg08904630',c(2:4)]*100
# logFC CI.L CI.R
# cg08904630 0.4763335 0.3358858 0.6167811
DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg22799518',c(2:4)]*100
# logFC CI.L CI.R
# cg22799518 -0.2005144 -0.4265598 0.02553097
DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg01744822',c(2:4)]*100
# logFC CI.L CI.R
# cg01744822 -1.662075 -2.293577 -1.030573
DMP_Mn_F_age7_beta[[3]][DMP_Mn_F_age7_beta[[3]]$cpg == 'cg15712310',c(2:4)]*100
# logFC CI.L CI.R
# cg15712310 -0.9650864 -1.858607 -0.07156615
rm(DMP_Mn_F_age7_beta);gc()
# Sensitivity analysis only including overlap with cord blood infants
DMP_Mn_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 85
# Adjusted, p<0.05: 45254
# Adjusted, FDR<0.05: 433
# Adjusted, pBonf<0.05: 7
# Adjusted, lambda: 1.388295
# Number of DMRs identified: 25
rm(DMP_Mn_F_age7_cordoverlap);gc()
FDR-significant DMPs
|
|
cpg
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
48627
|
cg02920176
|
0.28 (0.17 ,0.38)
|
5.13
|
7e-07
|
0.0478732
|
0.2859
|
chr7
|
36404389
|
KIAA0895;KIAA0895
|
|
90890
|
cg05613017
|
0.26 (0.16 ,0.36)
|
5.32
|
7e-07
|
0.0478732
|
0.2854
|
chr12
|
65589446
|
LEMD3;LEMD3
|
|
170758
|
cg11063328
|
-0.26 (-0.33 ,-0.18)
|
-6.00
|
0e+00
|
0.0003803
|
0.0005
|
chr11
|
18343203
|
GTF2H1;HPS5;HPS5;HPS5;GTF2H1
|
|
250921
|
cg16675029
|
-0.11 (-0.15 ,-0.07)
|
-6.42
|
7e-07
|
0.0478732
|
0.2872
|
chr8
|
6565876
|
AGPAT5
|
|
286677
|
cg19425870
|
-0.25 (-0.32 ,-0.17)
|
-6.45
|
0e+00
|
0.0003803
|
0.0008
|
chr11
|
3876808
|
STIM1
|
|
324070
|
cg22396353
|
-0.15 (-0.2 ,-0.1)
|
-6.10
|
1e-07
|
0.0170936
|
0.0513
|
chr22
|
46692687
|
GTSE1;GTSE1;CN5H6.4
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
6
|
3849410
|
3849690
|
5e-07
|
280
|
5e-07
|
0.0007357
|
10
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F_smk/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F_smk/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_F_smk/Mn_log2_manhattan_DMP_adj.png")

Mn, male
DMP_Mn_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M_smk')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 14905
# Unadjusted, FDR<0.05: 27
# Unadjusted, pBonf<0.05: 9
# Adjusted, N = 175
# Adjusted, p<0.05: 18986
# Adjusted, FDR<0.05: 30
# Adjusted, pBonf<0.05: 13
# Adjusted, lambda: 0.9800403
# Number of DMRs identified: 14
DMP_Mn_M_age7[[3]] = NULL
# limma on Beta-values
DMP_Mn_M_age7_beta = run_EWAS(DNAm = ComBat.Betas.Metals, pheno = pDatAge7Metal_M, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M_smk_beta')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 14417
# Unadjusted, FDR<0.05: 227
# Unadjusted, pBonf<0.05: 82
# Adjusted, N = 175
# Adjusted, p<0.05: 18971
# Adjusted, FDR<0.05: 257
# Adjusted, pBonf<0.05: 85
# Adjusted, lambda: 0.9273041
# Number of DMRs identified: 27
DMP_Mn_M_age7_beta[[3]][DMP_Mn_M_age7_beta[[3]]$cpg == 'cg03763518',c(2:4)]*100
# logFC CI.L CI.R
# cg03763518 -3.025927 -4.557014 -1.49484
DMP_Mn_M_age7_beta[[3]][DMP_Mn_M_age7_beta[[3]]$cpg == 'cg02042823',c(2:4)]*100
# logFC CI.L CI.R
# cg02042823 1.815752 0.5050111 3.126493
rm(DMP_Mn_M_age7_beta);gc()
# Sensitivity analysis only including overlap with cord blood infants
DMP_Mn_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Mn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 104
# Adjusted, p<0.05: 15442
# Adjusted, FDR<0.05: 45
# Adjusted, pBonf<0.05: 12
# Adjusted, lambda: 0.8201768
# Number of DMRs identified: 16
FDR-significant DMPs
|
|
cpg
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
56695
|
cg03425412
|
-0.22 (-0.31 ,-0.14)
|
-5.94
|
1.1e-06
|
0.0200355
|
0.4408
|
chr20
|
21500337
|
|
|
68153
|
cg04143120
|
0.41 (0.27 ,0.55)
|
6.79
|
0.0e+00
|
0.0009703
|
0.0068
|
chr11
|
72968848
|
|
|
79809
|
cg04885068
|
0.19 (0.12 ,0.25)
|
6.47
|
1.0e-07
|
0.0034580
|
0.0386
|
chr1
|
9099298
|
SLC2A5;SLC2A5
|
|
82300
|
cg05041382
|
-0.12 (-0.17 ,-0.07)
|
-6.39
|
2.4e-06
|
0.0357914
|
0.9313
|
chr13
|
50366546
|
KPNA3
|
|
85445
|
cg05249026
|
-0.16 (-0.22 ,-0.1)
|
-2.36
|
3.0e-07
|
0.0071381
|
0.1213
|
chr16
|
11031524
|
DEXI
|
|
97510
|
cg06051716
|
0.36 (0.24 ,0.47)
|
6.49
|
0.0e+00
|
0.0002792
|
0.0015
|
chr6
|
169225783
|
|
|
107728
|
cg06756211
|
-0.21 (-0.27 ,-0.14)
|
-6.05
|
0.0e+00
|
0.0002792
|
0.0017
|
chr1
|
223936799
|
CAPN2;CAPN2
|
|
109948
|
cg06883949
|
-0.12 (-0.17 ,-0.07)
|
-6.47
|
8.0e-07
|
0.0151676
|
0.3034
|
chr4
|
1795240
|
FGFR3;FGFR3;FGFR3
|
|
128092
|
cg08072480
|
-0.14 (-0.19 ,-0.08)
|
-6.61
|
2.0e-06
|
0.0320210
|
0.7829
|
chr11
|
65292666
|
SCYL1;SCYL1
|
|
157031
|
cg10088075
|
-0.11 (-0.16 ,-0.07)
|
-6.21
|
3.8e-06
|
0.0499734
|
1.0000
|
chr16
|
30407103
|
ZNF48;ZNF48
|
|
176390
|
cg11480534
|
0.4 (0.24 ,0.55)
|
5.84
|
9.0e-07
|
0.0173628
|
0.3646
|
chr11
|
62255850
|
AHNAK
|
|
176843
|
cg11521780
|
-0.14 (-0.18 ,-0.09)
|
-5.77
|
0.0e+00
|
0.0015624
|
0.0125
|
chr12
|
53693949
|
C12orf10
|
|
180100
|
cg11755803
|
0.4 (0.24 ,0.56)
|
5.79
|
1.7e-06
|
0.0288393
|
0.6633
|
chr12
|
129000542
|
TMEM132C
|
|
192975
|
cg12700904
|
-0.1 (-0.14 ,-0.06)
|
-5.94
|
2.9e-06
|
0.0388460
|
1.0000
|
chr3
|
13590720
|
FBLN2;FBLN2
|
|
194538
|
cg12828656
|
-0.15 (-0.2 ,-0.1)
|
-0.50
|
0.0e+00
|
0.0002792
|
0.0012
|
chr5
|
132577108
|
FSTL4
|
|
209344
|
cg13834844
|
-0.15 (-0.22 ,-0.09)
|
-5.13
|
2.0e-06
|
0.0320210
|
0.8005
|
chr10
|
102415320
|
|
|
209541
|
cg13848566
|
-0.17 (-0.22 ,-0.11)
|
-6.36
|
2.0e-07
|
0.0041615
|
0.0624
|
chr9
|
89561175
|
GAS1
|
|
214672
|
cg14149680
|
-0.29 (-0.38 ,-0.2)
|
-6.35
|
0.0e+00
|
0.0001372
|
0.0004
|
chr11
|
2187632
|
TH;TH;TH
|
|
249118
|
cg16560774
|
-0.17 (-0.22 ,-0.11)
|
-6.46
|
0.0e+00
|
0.0018682
|
0.0168
|
chr17
|
79373381
|
BAHCC1
|
|
286458
|
cg19407717
|
0.5 (0.35 ,0.64)
|
4.03
|
0.0e+00
|
0.0000364
|
0.0001
|
chr2
|
1544120
|
TPO;TPO;TPO;TPO
|
|
287817
|
cg19511862
|
-0.1 (-0.14 ,-0.06)
|
-6.26
|
5.0e-07
|
0.0106449
|
0.2023
|
chr12
|
125478458
|
BRI3BP
|
|
289598
|
cg19641404
|
-0.11 (-0.16 ,-0.07)
|
-5.87
|
2.5e-06
|
0.0357914
|
0.9762
|
chr2
|
232826272
|
DIS3L2
|
|
299702
|
cg20414082
|
0.26 (0.16 ,0.36)
|
3.20
|
4.0e-07
|
0.0085706
|
0.1543
|
chr1
|
203002593
|
|
|
300828
|
cg20504533
|
-0.22 (-0.28 ,-0.15)
|
-5.85
|
0.0e+00
|
0.0000364
|
0.0001
|
chr17
|
15848253
|
ADORA2B;ADORA2B
|
|
326031
|
cg22563312
|
-0.17 (-0.22 ,-0.11)
|
-6.27
|
1.0e-07
|
0.0034580
|
0.0450
|
chr5
|
179334739
|
TBC1D9B;TBC1D9B
|
|
327739
|
cg22702772
|
-0.15 (-0.2 ,-0.1)
|
-6.69
|
1.0e-07
|
0.0034580
|
0.0430
|
chr3
|
48699012
|
CELSR3
|
|
347861
|
cg24196240
|
0.42 (0.27 ,0.56)
|
5.27
|
2.0e-07
|
0.0041615
|
0.0617
|
chr21
|
36096009
|
NCRNA00160
|
|
357841
|
cg24948962
|
-0.22 (-0.29 ,-0.14)
|
-5.44
|
1.0e-07
|
0.0034580
|
0.0385
|
chr18
|
2906032
|
EMILIN2
|
|
360532
|
cg25152909
|
0.43 (0.27 ,0.58)
|
6.08
|
2.0e-07
|
0.0043902
|
0.0702
|
chr5
|
172566090
|
C5orf41
|
|
364427
|
cg25466588
|
-0.09 (-0.13 ,-0.06)
|
-5.90
|
2.5e-06
|
0.0357914
|
1.0000
|
chr3
|
23958904
|
NKIRAS1;RPL15
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
1
|
161008461
|
161008977
|
0.0000000
|
516
|
0.0000000
|
0.0000000
|
8
|
|
19
|
21657528
|
21658001
|
0.0000000
|
473
|
0.0000000
|
0.0000000
|
5
|
|
19
|
10736005
|
10736117
|
0.0000000
|
112
|
0.0000000
|
0.0000055
|
5
|
|
20
|
5485244
|
5485511
|
0.0000000
|
267
|
0.0000000
|
0.0000036
|
6
|
|
4
|
79971176
|
79971432
|
0.0000000
|
256
|
0.0000000
|
0.0000079
|
4
|
|
20
|
35169593
|
35169886
|
0.0000000
|
293
|
0.0000000
|
0.0000081
|
5
|
|
1
|
9099280
|
9099462
|
0.0000001
|
182
|
0.0000002
|
0.0001641
|
3
|
|
6
|
26018002
|
26018185
|
0.0000001
|
183
|
0.0000002
|
0.0002514
|
6
|
|
16
|
30572738
|
30573013
|
0.0000001
|
275
|
0.0000002
|
0.0001883
|
5
|
|
3
|
39543966
|
39544192
|
0.0000032
|
226
|
0.0000045
|
0.0055785
|
2
|
|
15
|
91473090
|
91473365
|
0.0000066
|
275
|
0.0000084
|
0.0094606
|
4
|
|
19
|
12444612
|
12444741
|
0.0000102
|
129
|
0.0000119
|
0.0307855
|
5
|
|
6
|
37616597
|
37616686
|
0.0000933
|
89
|
0.0001005
|
0.3386856
|
2
|
|
2
|
3642628
|
3642634
|
0.0032946
|
6
|
0.0032946
|
1.0000000
|
2
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M_smk/Mn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M_smk/Mn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Mn_M_smk/Mn_log2_manhattan_DMP_adj.png")

Pb
DMP_Pb_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Pb_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_smk')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 13157
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 333
# Adjusted, p<0.05: 19598
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.056675
# Number of DMRs identified: 6
DMP_Pb_age7[[3]] = NULL
# limma on Beta-values
DMP_Pb_age7_beta = run_EWAS(DNAm = ComBat.Betas.Metals, pheno = pDatAge7Metal, var = 'Pb_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_smk_beta')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 13578
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 333
# Adjusted, p<0.05: 20646
# Adjusted, FDR<0.05: 1
# Adjusted, pBonf<0.05: 1
# Adjusted, lambda: 1.092762
# Number of DMRs identified: 6
DMP_Pb_age7_beta[[3]][DMP_Pb_age7_beta[[3]]$cpg == 'cg20608990',c(2:4)]*100
# logFC CI.L CI.R
# cg20608990 -1.564971 -2.725569 -0.4043731
rm(DMP_Pb_age7_beta);gc()
# Sensitivity analysis only including overlap with cord blood infants
DMP_Pb_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Pb_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 189
# Adjusted, p<0.05: 43924
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.730948
# Number of identified DMR: 0
rm(DMP_Pb_age7_cordoverlap);gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
10
|
135051021
|
135051581
|
0e+00
|
560
|
0e+00
|
0.0000000
|
11
|
|
22
|
45704901
|
45705265
|
0e+00
|
364
|
0e+00
|
0.0000000
|
7
|
|
22
|
19746155
|
19746368
|
0e+00
|
213
|
0e+00
|
0.0000225
|
3
|
|
3
|
130745441
|
130745685
|
0e+00
|
244
|
0e+00
|
0.0000389
|
10
|
|
7
|
155283139
|
155283424
|
0e+00
|
285
|
1e-07
|
0.0000621
|
3
|
|
14
|
104690039
|
104690244
|
1e-07
|
205
|
1e-07
|
0.0002063
|
5
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_smk/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_smk/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_smk/Pb_log2_manhattan_DMP_adj.png")

Pb, female
DMP_Pb_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Pb_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F_smk')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 10571
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 12151
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.7522295
# Number of identified DMR: 0
DMP_Pb_F_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Pb_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Pb_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 85
# Adjusted, p<0.05: 15685
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9341139
# Number of identified DMR: 0
rm(DMP_Pb_F_age7_cordoverlap);gc()
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F_smk/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F_smk/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_F_smk/Pb_log2_manhattan_DMP_adj.png")

Pb, male
DMP_Pb_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Pb_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M_smk')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 18362
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 175
# Adjusted, p<0.05: 14153
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9440498
# Number of DMRs identified: 4
DMP_Pb_M_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Pb_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Pb_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 104
# Adjusted, p<0.05: 21607
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 1.165536
# Number of DMRs identified: 6
rm(DMP_Pb_M_age7_cordoverlap);gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
6
|
33084769
|
33084985
|
0
|
216
|
0
|
1.00e-07
|
11
|
|
1
|
68512649
|
68513063
|
0
|
414
|
0
|
3.00e-07
|
7
|
|
6
|
31148369
|
31148748
|
0
|
379
|
0
|
2.70e-06
|
13
|
|
22
|
45704987
|
45705265
|
0
|
278
|
0
|
6.82e-05
|
5
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M_smk/Pb_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M_smk/Pb_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Pb_M_smk/Pb_log2_manhattan_DMP_adj.png")

Se
DMP_Se_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Se_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_smk')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 17270
# Unadjusted, FDR<0.05: 1
# Unadjusted, pBonf<0.05: 1
# Adjusted, N = 333
# Adjusted, p<0.05: 20324
# Adjusted, FDR<0.05: 4
# Adjusted, pBonf<0.05: 1
# Adjusted, lambda: 0.9736407
# Number of DMRs identified: 3
DMP_Se_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Se_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Se_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 189
# Adjusted, p<0.05: 16337
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8902786
# Number of DMRs identified: 2
FDR-significant DMPs
|
|
cpg
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
138326
|
cg08760128
|
0.2 (0.13 ,0.28)
|
6.73
|
4e-07
|
0.0460845
|
0.1487
|
chr16
|
4723507
|
MGRN1;MGRN1;MGRN1;MGRN1
|
|
157990
|
cg10145926
|
0.55 (0.35 ,0.75)
|
5.31
|
1e-07
|
0.0286748
|
0.0573
|
chr14
|
95875792
|
C14orf139
|
|
202444
|
cg13434714
|
-0.42 (-0.57 ,-0.28)
|
-5.77
|
0e+00
|
0.0077289
|
0.0077
|
chr12
|
6936787
|
LEPREL2
|
|
381104
|
cg26708724
|
0.59 (0.36 ,0.81)
|
6.73
|
5e-07
|
0.0460845
|
0.1843
|
chr4
|
187509785
|
FAT1
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
47091977
|
47092178
|
0
|
201
|
0
|
4.00e-06
|
4
|
|
19
|
50194119
|
50194252
|
0
|
133
|
0
|
1.57e-05
|
5
|
|
6
|
49681177
|
49681391
|
0
|
214
|
0
|
2.89e-05
|
7
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_smk/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_smk/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_smk/Se_log2_manhattan_DMP_adj.png")

Se, female
DMP_Se_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Se_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F_smk')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 26254
# Unadjusted, FDR<0.05: 9
# Unadjusted, pBonf<0.05: 2
# Adjusted, N = 158
# Adjusted, p<0.05: 16049
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9296273
# Number of DMRs identified: 3
DMP_Se_F_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Se_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Se_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 85
# Adjusted, p<0.05: 16966
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9935428
# Number of DMRs identified: 5
rm(DMP_Se_F_age7_cordoverlap);gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
10
|
38146245
|
38146671
|
0
|
426
|
0
|
4.00e-07
|
9
|
|
6
|
49681177
|
49681391
|
0
|
214
|
0
|
1.00e-06
|
7
|
|
10
|
38299241
|
38299574
|
0
|
333
|
0
|
1.83e-05
|
9
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F_smk/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F_smk/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_F_smk/Se_log2_manhattan_DMP_adj.png")

Se, male
DMP_Se_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Se_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M_smk')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 15593
# Unadjusted, FDR<0.05: 42
# Unadjusted, pBonf<0.05: 12
# Adjusted, N = 175
# Adjusted, p<0.05: 13808
# Adjusted, FDR<0.05: 20
# Adjusted, pBonf<0.05: 6
# Adjusted, lambda: 0.7972324
# Number of DMRs identified: 3
DMP_Se_M_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Se_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Se_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)
Adjusted, N = 104
Adjusted, p<0.05: 13747
Adjusted, FDR<0.05: 0
Adjusted, pBonf<0.05: 0
Adjusted, lambda: 0.8042952
Number of DMRs identified: 4
rm(DMP_Se_M_age7_cordoverlap);gc()
FDR-significant DMPs
|
|
cpg
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
5657
|
cg00326183
|
0.4 (0.24 ,0.56)
|
2.20
|
1.8e-06
|
0.0389133
|
0.7004
|
chr2
|
241808259
|
AGXT;AGXT
|
|
15593
|
cg00908120
|
0.6 (0.36 ,0.83)
|
6.29
|
1.1e-06
|
0.0299539
|
0.4194
|
chr16
|
72872925
|
ZFHX3;ZFHX3
|
|
17338
|
cg01007589
|
0.77 (0.47 ,1.07)
|
4.79
|
1.4e-06
|
0.0359853
|
0.5398
|
chr19
|
49894178
|
CCDC155
|
|
26849
|
cg01588060
|
-0.27 (-0.38 ,-0.17)
|
-5.90
|
8.0e-07
|
0.0259001
|
0.3108
|
chr6
|
2245749
|
GMDS;GMDS
|
|
76780
|
cg04692924
|
-0.59 (-0.8 ,-0.38)
|
-6.58
|
1.0e-07
|
0.0071719
|
0.0547
|
chr1
|
161720042
|
DUSP12
|
|
82479
|
cg05051957
|
-0.66 (-0.88 ,-0.44)
|
-5.61
|
0.0e+00
|
0.0015014
|
0.0046
|
chr8
|
141522459
|
CHRAC1;CHRAC1
|
|
107200
|
cg06723863
|
-0.34 (-0.47 ,-0.22)
|
-5.99
|
1.0e-07
|
0.0071719
|
0.0574
|
chr16
|
68270129
|
ESRP2;ESRP2
|
|
121260
|
cg07599133
|
-0.34 (-0.48 ,-0.21)
|
-5.96
|
1.8e-06
|
0.0389133
|
0.6939
|
chr19
|
35068628
|
LOC643719
|
|
175991
|
cg11443888
|
0.28 (0.17 ,0.39)
|
2.36
|
1.9e-06
|
0.0392822
|
0.7464
|
chr6
|
44244590
|
TMEM151B
|
|
178008
|
cg11608893
|
0.84 (0.55 ,1.12)
|
6.08
|
1.0e-07
|
0.0039836
|
0.0199
|
chr6
|
32059542
|
TNXB
|
|
186947
|
cg12243007
|
0.44 (0.27 ,0.61)
|
-0.77
|
1.0e-06
|
0.0289023
|
0.3757
|
chr17
|
184018
|
RPH3AL
|
|
195368
|
cg12897502
|
-0.84 (-1.16 ,-0.52)
|
6.10
|
6.0e-07
|
0.0204295
|
0.2247
|
chr8
|
67425316
|
C8orf46
|
|
202444
|
cg13434714
|
-0.63 (-0.81 ,-0.45)
|
-5.78
|
0.0e+00
|
0.0000186
|
0.0000
|
chr12
|
6936787
|
LEPREL2
|
|
250632
|
cg16656826
|
0.29 (0.18 ,0.41)
|
0.14
|
1.5e-06
|
0.0376409
|
0.6023
|
chr5
|
159343871
|
ADRA1B;ADRA1B
|
|
273355
|
cg18377660
|
0.71 (0.45 ,0.97)
|
5.65
|
2.0e-07
|
0.0089756
|
0.0808
|
chr1
|
57535755
|
DAB1
|
|
281545
|
cg19005275
|
0.59 (0.37 ,0.81)
|
4.29
|
4.0e-07
|
0.0162778
|
0.1628
|
chr12
|
113588263
|
CCDC42B
|
|
311691
|
cg21373263
|
0.82 (0.55 ,1.1)
|
3.29
|
0.0e+00
|
0.0015014
|
0.0060
|
chr10
|
126751982
|
CTBP2;CTBP2
|
|
359398
|
cg25067702
|
-0.64 (-0.87 ,-0.41)
|
-6.40
|
1.0e-07
|
0.0065970
|
0.0396
|
chr17
|
70723227
|
SLC39A11;SLC39A11
|
|
375884
|
cg26342676
|
0.61 (0.37 ,0.86)
|
4.56
|
2.3e-06
|
0.0454735
|
0.9095
|
chr14
|
37639757
|
SLC25A21;SLC25A21;LOC100129794
|
|
381104
|
cg26708724
|
1.01 (0.73 ,1.3)
|
6.72
|
0.0e+00
|
0.0000174
|
0.0000
|
chr4
|
187509785
|
FAT1
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
70723226
|
70723386
|
0e+00
|
160
|
0e+00
|
0.0000001
|
2
|
|
4
|
24796918
|
24797176
|
0e+00
|
258
|
0e+00
|
0.0000241
|
6
|
|
10
|
121578383
|
121578639
|
1e-07
|
256
|
1e-07
|
0.0001184
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M_smk/Se_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M_smk/Se_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Se_M_smk/Se_log2_manhattan_DMP_adj.png")

Zn
DMP_Zn_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal, var = 'Zn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_smk')
# Unadjusted, N = 333
# Unadjusted, p<0.05: 12854
# Unadjusted, FDR<0.05: 1
# Unadjusted, pBonf<0.05: 1
# Adjusted, N = 333
# Adjusted, p<0.05: 23322
# Adjusted, FDR<0.05: 13
# Adjusted, pBonf<0.05: 3
# Adjusted, lambda: 1.103711
# Number of DMRs identified: 13
DMP_Zn_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Zn_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_cord, var = 'Zn_log2', covar = c('female_d', 'race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 189
# Adjusted, p<0.05: 14814
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.8661672
# Number of DMRs identified: 5
rm(DMP_Zn_age7_cordoverlap);gc()
FDR-significant DMPs
|
|
cpg
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
1551
|
cg00082497
|
-0.28 (-0.38 ,-0.18)
|
-5.32
|
1.0e-07
|
0.0122297
|
0.0337
|
chr1
|
32802133
|
MARCKSL1
|
|
15593
|
cg00908120
|
0.49 (0.31 ,0.67)
|
6.26
|
3.0e-07
|
0.0170276
|
0.1166
|
chr16
|
72872925
|
ZFHX3;ZFHX3
|
|
66105
|
cg04015129
|
0.65 (0.4 ,0.91)
|
4.28
|
8.0e-07
|
0.0307007
|
0.3136
|
chr10
|
1058036
|
GTPBP4
|
|
90290
|
cg05573434
|
0.41 (0.26 ,0.57)
|
-3.15
|
3.0e-07
|
0.0170276
|
0.1192
|
chr4
|
7648540
|
SORCS2
|
|
107200
|
cg06723863
|
-0.25 (-0.35 ,-0.15)
|
-5.98
|
1.6e-06
|
0.0495322
|
0.6439
|
chr16
|
68270129
|
ESRP2;ESRP2
|
|
133940
|
cg08459368
|
0.59 (0.38 ,0.81)
|
2.65
|
1.0e-07
|
0.0122297
|
0.0395
|
chr11
|
61974948
|
SCGB2A1
|
|
165306
|
cg10653573
|
0.82 (0.5 ,1.14)
|
5.43
|
7.0e-07
|
0.0307007
|
0.2910
|
chr8
|
141347297
|
TRAPPC9;TRAPPC9
|
|
202444
|
cg13434714
|
-0.49 (-0.64 ,-0.33)
|
-5.77
|
0.0e+00
|
0.0012560
|
0.0013
|
chr12
|
6936787
|
LEPREL2
|
|
234745
|
cg15528091
|
-0.31 (-0.43 ,-0.19)
|
-6.36
|
9.0e-07
|
0.0307007
|
0.3391
|
chr19
|
18119069
|
ARRDC2;ARRDC2;ARRDC2
|
|
248112
|
cg16496814
|
0.21 (0.13 ,0.3)
|
5.21
|
6.0e-07
|
0.0299711
|
0.2398
|
chr11
|
9778721
|
|
|
281636
|
cg19011752
|
0.25 (0.15 ,0.34)
|
-2.54
|
9.0e-07
|
0.0307007
|
0.3684
|
chr21
|
45772638
|
TRPM2
|
|
338217
|
cg23477849
|
0.26 (0.16 ,0.36)
|
4.88
|
2.0e-07
|
0.0122297
|
0.0600
|
chr19
|
5698492
|
LONP1
|
|
370410
|
cg25954729
|
-0.22 (-0.29 ,-0.14)
|
-6.34
|
2.0e-07
|
0.0122297
|
0.0611
|
chr11
|
66610784
|
RCE1;C11orf80;RCE1
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
12
|
54070516
|
54070610
|
0.0000000
|
94
|
0.0000000
|
0.0000053
|
5
|
|
19
|
18118799
|
18119069
|
0.0000000
|
270
|
0.0000000
|
0.0000104
|
3
|
|
10
|
124638975
|
124639260
|
0.0000000
|
285
|
0.0000001
|
0.0000244
|
12
|
|
6
|
32063990
|
32064258
|
0.0000001
|
268
|
0.0000002
|
0.0000840
|
12
|
|
4
|
7648539
|
7648627
|
0.0000001
|
88
|
0.0000002
|
0.0003269
|
2
|
|
8
|
41655672
|
41655894
|
0.0000001
|
222
|
0.0000002
|
0.0002414
|
4
|
|
6
|
41168800
|
41169049
|
0.0000001
|
249
|
0.0000002
|
0.0002270
|
6
|
|
17
|
1395863
|
1396123
|
0.0000002
|
260
|
0.0000002
|
0.0002710
|
5
|
|
12
|
54385274
|
54385526
|
0.0000002
|
252
|
0.0000002
|
0.0002813
|
4
|
|
17
|
79503641
|
79503877
|
0.0000002
|
236
|
0.0000002
|
0.0003092
|
4
|
|
22
|
45704987
|
45705042
|
0.0000002
|
55
|
0.0000003
|
0.0015642
|
4
|
|
20
|
25129506
|
25129562
|
0.0000016
|
56
|
0.0000017
|
0.0113002
|
5
|
|
20
|
35169593
|
35169846
|
0.0004394
|
253
|
0.0004394
|
0.4960606
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_smk/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_smk/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_smk/Zn_log2_manhattan_DMP_adj.png")

Zn, female
DMP_Zn_F_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F, var = 'Zn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F_smk')
# Unadjusted, N = 158
# Unadjusted, p<0.05: 12830
# Unadjusted, FDR<0.05: 0
# Unadjusted, pBonf<0.05: 0
# Adjusted, N = 158
# Adjusted, p<0.05: 17367
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.9501586
# Number of DMRs identified: 1
DMP_Zn_F_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Zn_F_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_F_cord, var = 'Zn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 85
# Adjusted, p<0.05: 12704
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.7959756
# Number of DMRs identified: 2
rm(DMP_Zn_F_age7_cordoverlap);gc()
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
11
|
73357018
|
73357396
|
0
|
378
|
0
|
0
|
8
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F_smk/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F_smk/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_F_smk/Zn_log2_manhattan_DMP_adj.png")

Zn, male
DMP_Zn_M_age7 = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M, var = 'Zn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M_smk')
# Unadjusted, N = 175
# Unadjusted, p<0.05: 16787
# Unadjusted, FDR<0.05: 36
# Unadjusted, pBonf<0.05: 8
# Adjusted, N = 175
# Adjusted, p<0.05: 14614
# Adjusted, FDR<0.05: 37
# Adjusted, pBonf<0.05: 3
# Adjusted, lambda: 0.8610523
# Number of DMRs identified: 16
DMP_Zn_M_age7[[3]] = NULL
# Sensitivity analysis only including overlap with cord blood infants
DMP_Zn_M_age7_cordoverlap = run_EWAS(DNAm = ComBat.Mvalues.Metals, pheno = pDatAge7Metal_M_cord, var = 'Zn_log2', covar = c('race_child2', 'age_yrs_7y_blood', 'age_mom_enroll_d', 'bmi_mom_prepreg_d', 'coll_grad', 'nullip', 'gt70k', 'smk_preg2', 'Bcell_S_7y', 'CD4T_S_7y', 'CD8T_S_7y', 'Neu_S_7y', 'Mono_S_7y', 'NK_S_7y'), anno = anno, path = '/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M_smk_cordoverlap', unadj = FALSE, plot = FALSE)
# Adjusted, N = 104
# Adjusted, p<0.05: 14686
# Adjusted, FDR<0.05: 0
# Adjusted, pBonf<0.05: 0
# Adjusted, lambda: 0.907332
# Number of DMRs identified: 5
rm(DMP_Zn_M_age7_cordoverlap);gc()
FDR-significant DMPs
|
|
cpg
|
logFC_CI
|
AveExpr
|
P.Value
|
adj.P.Val
|
adj.P.Val.bonf
|
chr
|
pos
|
gene
|
|
15593
|
cg00908120
|
0.79 (0.52 ,1.06)
|
6.29
|
0.0e+00
|
0.0059562
|
0.0162
|
chr16
|
72872925
|
ZFHX3;ZFHX3
|
|
17338
|
cg01007589
|
0.92 (0.56 ,1.28)
|
4.79
|
1.1e-06
|
0.0188947
|
0.4346
|
chr19
|
49894178
|
CCDC155
|
|
18335
|
cg01063965
|
-0.27 (-0.38 ,-0.16)
|
-6.44
|
4.3e-06
|
0.0462438
|
1.0000
|
chr11
|
695461
|
TMEM80;TMEM80;DEAF1;DEAF1
|
|
24635
|
cg01447660
|
0.42 (0.25 ,0.59)
|
-0.92
|
2.9e-06
|
0.0363415
|
1.0000
|
chr2
|
69152678
|
|
|
36678
|
cg02196294
|
-0.29 (-0.41 ,-0.17)
|
-5.41
|
4.0e-06
|
0.0443654
|
1.0000
|
chr6
|
39197260
|
KCNK5
|
|
41497
|
cg02490920
|
0.39 (0.24 ,0.54)
|
1.34
|
1.1e-06
|
0.0188947
|
0.4228
|
chr3
|
50304406
|
SEMA3B;SEMA3B
|
|
45187
|
cg02711608
|
0.54 (0.34 ,0.74)
|
-2.09
|
3.0e-07
|
0.0124570
|
0.1004
|
chr19
|
47287964
|
SLC1A5;SLC1A5;SLC1A5;SLC1A5
|
|
49479
|
cg02968175
|
0.33 (0.2 ,0.45)
|
5.76
|
7.0e-07
|
0.0136814
|
0.2736
|
chr16
|
4690020
|
MGRN1;MGRN1;MGRN1;MGRN1
|
|
55565
|
cg03352332
|
0.89 (0.55 ,1.22)
|
5.54
|
5.0e-07
|
0.0124570
|
0.1869
|
chr3
|
186360953
|
FETUB
|
|
66105
|
cg04015129
|
0.86 (0.55 ,1.18)
|
4.27
|
3.0e-07
|
0.0124570
|
0.0993
|
chr10
|
1058036
|
GTPBP4
|
|
71895
|
cg04374006
|
0.27 (0.16 ,0.37)
|
-0.27
|
2.3e-06
|
0.0311662
|
0.9038
|
chr19
|
33556395
|
RHPN2
|
|
72385
|
cg04406071
|
-0.32 (-0.45 ,-0.2)
|
-6.07
|
7.0e-07
|
0.0136814
|
0.2633
|
chr17
|
59489784
|
C17orf82
|
|
76780
|
cg04692924
|
-0.66 (-0.91 ,-0.41)
|
-6.58
|
8.0e-07
|
0.0148121
|
0.3111
|
chr1
|
161720042
|
DUSP12
|
|
82479
|
cg05051957
|
-0.65 (-0.92 ,-0.39)
|
-5.61
|
3.1e-06
|
0.0382640
|
1.0000
|
chr8
|
141522459
|
CHRAC1;CHRAC1
|
|
107200
|
cg06723863
|
-0.36 (-0.51 ,-0.21)
|
-5.99
|
3.3e-06
|
0.0382640
|
1.0000
|
chr16
|
68270129
|
ESRP2;ESRP2
|
|
117957
|
cg07380021
|
-0.66 (-0.91 ,-0.41)
|
-5.43
|
4.0e-07
|
0.0124570
|
0.1536
|
chr1
|
206755252
|
RASSF5;RASSF5;RASSF5
|
|
138326
|
cg08760128
|
0.36 (0.23 ,0.49)
|
6.73
|
1.0e-07
|
0.0124570
|
0.0590
|
chr16
|
4723507
|
MGRN1;MGRN1;MGRN1;MGRN1
|
|
159790
|
cg10266648
|
1.03 (0.62 ,1.44)
|
5.98
|
1.8e-06
|
0.0268172
|
0.6972
|
chr2
|
106560529
|
|
|
165306
|
cg10653573
|
1.41 (0.89 ,1.93)
|
5.37
|
3.0e-07
|
0.0124570
|
0.1021
|
chr8
|
141347297
|
TRAPPC9;TRAPPC9
|
|
168880
|
cg10923018
|
0.31 (0.18 ,0.43)
|
2.73
|
3.2e-06
|
0.0382640
|
1.0000
|
chr6
|
31743769
|
C6orf27
|
|
180170
|
cg11761483
|
-0.72 (-0.99 ,-0.45)
|
-5.60
|
4.0e-07
|
0.0124570
|
0.1584
|
chr17
|
70723386
|
SLC39A11;SLC39A11
|
|
202444
|
cg13434714
|
-0.83 (-1.04 ,-0.63)
|
-5.78
|
0.0e+00
|
0.0000001
|
0.0000
|
chr12
|
6936787
|
LEPREL2
|
|
216196
|
cg14230280
|
1.23 (0.74 ,1.72)
|
4.28
|
1.9e-06
|
0.0274435
|
0.7684
|
chr9
|
132502800
|
PTGES
|
|
248112
|
cg16496814
|
0.32 (0.2 ,0.44)
|
5.22
|
4.0e-07
|
0.0124570
|
0.1617
|
chr11
|
9778721
|
|
|
250632
|
cg16656826
|
0.35 (0.21 ,0.48)
|
0.14
|
1.9e-06
|
0.0273935
|
0.7396
|
chr5
|
159343871
|
ADRA1B;ADRA1B
|
|
268589
|
cg18037826
|
0.41 (0.26 ,0.57)
|
4.29
|
6.0e-07
|
0.0136814
|
0.2473
|
chr12
|
109273835
|
DAO
|
|
281545
|
cg19005275
|
0.75 (0.49 ,1.01)
|
4.29
|
0.0e+00
|
0.0059562
|
0.0179
|
chr12
|
113588263
|
CCDC42B
|
|
288096
|
cg19532212
|
0.75 (0.47 ,1.03)
|
4.42
|
3.0e-07
|
0.0124570
|
0.1355
|
chr17
|
56769430
|
TEX14;RAD51C;TEX14;RAD51C
|
|
311691
|
cg21373263
|
0.88 (0.55 ,1.21)
|
3.29
|
4.0e-07
|
0.0124570
|
0.1769
|
chr10
|
126751982
|
CTBP2;CTBP2
|
|
322216
|
cg22240394
|
1.22 (0.76 ,1.67)
|
6.82
|
5.0e-07
|
0.0124570
|
0.1825
|
chr3
|
186211630
|
|
|
324251
|
cg22413938
|
-0.39 (-0.55 ,-0.23)
|
-4.56
|
2.5e-06
|
0.0328489
|
0.9855
|
chr14
|
78447481
|
|
|
338217
|
cg23477849
|
0.38 (0.23 ,0.53)
|
4.90
|
1.6e-06
|
0.0255962
|
0.6399
|
chr19
|
5698492
|
LONP1
|
|
339781
|
cg23601521
|
0.8 (0.49 ,1.1)
|
4.87
|
6.0e-07
|
0.0136814
|
0.2553
|
chr2
|
50275179
|
NRXN1;NRXN1;NRXN1
|
|
370410
|
cg25954729
|
-0.3 (-0.41 ,-0.19)
|
-6.37
|
4.0e-07
|
0.0124570
|
0.1703
|
chr11
|
66610784
|
RCE1;C11orf80;RCE1
|
|
379632
|
cg26608798
|
0.4 (0.24 ,0.56)
|
0.58
|
1.6e-06
|
0.0255962
|
0.6283
|
chr16
|
33853544
|
|
|
381104
|
cg26708724
|
0.94 (0.58 ,1.29)
|
6.72
|
6.0e-07
|
0.0136814
|
0.2306
|
chr4
|
187509785
|
FAT1
|
|
392164
|
cg27503275
|
0.47 (0.28 ,0.66)
|
4.12
|
3.5e-06
|
0.0389303
|
1.0000
|
chr6
|
3880016
|
|
DMRs
|
chr
|
start
|
end
|
p
|
length
|
fdr
|
sidak
|
nprobe
|
|
17
|
70723226
|
70723386
|
0.0000000
|
160
|
0.0000000
|
0.0000015
|
2
|
|
10
|
121578136
|
121578639
|
0.0000000
|
503
|
0.0000000
|
0.0000016
|
4
|
|
4
|
24796918
|
24797176
|
0.0000000
|
258
|
0.0000000
|
0.0000052
|
6
|
|
14
|
78447480
|
78447640
|
0.0000000
|
160
|
0.0000000
|
0.0000104
|
3
|
|
19
|
50194119
|
50194252
|
0.0000000
|
133
|
0.0000000
|
0.0000187
|
5
|
|
4
|
186732836
|
186733060
|
0.0000000
|
224
|
0.0000000
|
0.0000223
|
7
|
|
14
|
76734326
|
76734605
|
0.0000000
|
279
|
0.0000000
|
0.0000293
|
5
|
|
21
|
45773781
|
45773997
|
0.0000000
|
216
|
0.0000001
|
0.0000492
|
2
|
|
5
|
135416204
|
135416613
|
0.0000000
|
409
|
0.0000001
|
0.0000444
|
9
|
|
11
|
63679431
|
63679637
|
0.0000001
|
206
|
0.0000001
|
0.0001629
|
2
|
|
20
|
62716331
|
62716606
|
0.0000001
|
275
|
0.0000002
|
0.0001988
|
4
|
|
17
|
78549323
|
78549371
|
0.0000002
|
48
|
0.0000002
|
0.0013191
|
3
|
|
5
|
1868136
|
1868357
|
0.0000004
|
221
|
0.0000005
|
0.0007748
|
4
|
|
22
|
45704987
|
45705042
|
0.0000016
|
55
|
0.0000018
|
0.0110616
|
4
|
|
5
|
176755392
|
176755449
|
0.0000113
|
57
|
0.0000120
|
0.0749153
|
2
|
|
2
|
88583556
|
88583805
|
0.0001352
|
249
|
0.0001352
|
0.1927662
|
3
|
knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M_smk/Zn_log2_QQ_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M_smk/Zn_log2_volcano_DMP_adj.png")

knitr::include_graphics("/Users/annebozack/Documents/Cardenas/viva_DNAm_metals_local/Age7_adjBloodAge/Zn_M_smk/Zn_log2_manhattan_DMP_adj.png")
